Research workbench
Structure of the USP15 deubiquitinase domain in complex with a high- affinity first-generation ubv
Analyse Structure of the USP15 deubiquitinase domain in complex with a high- affinity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CRN
- Type
- protein
- Length
- 1,641 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 15; Ubiquitin variant 15.2
- EC
- 3.4.19.12
- UniProt
- Q9Y4E8
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 343 | 27% helix, 29% strand | Q9Y4E8 |
| B | Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 332 | 28% helix, 28% strand | Q9Y4E8 |
| C | Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 334 | 28% helix, 28% strand | Q9Y4E8 |
| D | Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 343 | 26% helix, 27% strand | Q9Y4E8 |
| E | Ubiquitin variant 15.2 | protein | 74 | 16% helix, 34% strand | — |
| F | Ubiquitin variant 15.2 | protein | 74 | 20% helix, 38% strand | — |
| G | Ubiquitin variant 15.2 | protein | 72 | 17% helix, 32% strand | — |
| H | Ubiquitin variant 15.2 | protein | 69 | 17% helix, 32% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.81 | 0.82 | 73 | empty |
| 2 | 803 | 0.81 | 0.84 | 72 | empty |
| 3 | 1055 | 0.81 | 0.82 | 83 | empty |
| 4 | 1086 | 0.80 | 0.82 | 73 | empty |
| 5 | 638 | 0.74 | 0.81 | 60 | empty |
Interfaces
8 interfaces between chains.
- C–E · 841 Ų buried · 12 hydrogen bonds · protein-protein
- D–G · 832 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 783 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 693 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 337 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6CRN · Structure of the USP15 deubiquitinase domain in complex with a high-affinity… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9Y4E8 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 15 (Q9Y4E8) · a predicted model of the same protein · chain B against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9Y4E8
- Elsewhere: RCSB PDB 6CRN · PDBe 6CRN · UniProt Q9Y4E8
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